Question: Xenopus genome files for RNAseq
gravatar for rob.costa1234
2.8 years ago by
United States
rob.costa1234250 wrote:

I have a clarification of which file to use from Xenbas (laevis). From this link- I think I will use primary gene models (FASTA) file for alignment and gene models (gff3) as GFF3 for annotation. Am I correct? I am doing RNAseq alignment with HISAT.

Here is screen shot of latest genome:

X. laevis v9.1 genome assembly[readme]FASTA Gene Model(s): [readme] primary gene models (gff3) primary gene models (FASTA) gene models (gff3) peptide(FASTA) For the latest versions browse theXenbase FTP site

rna-seq • 904 views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 2.8 years ago by rob.costa1234250
gravatar for Ron
2.8 years ago by
United States
Ron990 wrote:

I would use this file for the X. laevis 9.1 genome .

Note, you will have to unzip this as it is a .gz file.

And here is the GFF gene models file.

ADD COMMENTlink written 2.8 years ago by Ron990

Thanks do you have any suggestion where can I get these files for X tropicalis?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by rob.costa1234250

Try checking the links I pasted above.These are xenbase links only.

ADD REPLYlink written 2.8 years ago by Ron990
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